A Novel Peptide-Based SILAC Method to Identify the Posttranslational Modifications Provides Evidence for Unconventional Ubiquitination in the ER-Associated Degradation Pathway.

The endoplasmic reticulum-associated degradation (ERAD) pathway is responsible for disposing misfolded proteins from the endoplasmic reticulum by inducing their ubiquitination and degradation. Ubiquitination is conventionally observed on lysine residues and has been demonstrated on cysteine residues and protein N-termini. Ubiquitination is fundamental to the ERAD process; however, a mutant T-cell receptor α (TCRα) lacking lysine residues is targeted for the degradation by the ERAD pathway. We have shown that ubiquitination of lysine-less TCRα occurs on internal, non-lysine residues and that the same E3 ligase conjugates ubiquitin to TCRα in the presence or absence of lysine residues. Mass-spectrometry indicates that WT-TCRα is ubiquitinated on multiple lysine residues. Recent publications have provided indirect evidence that serine and threonine residues may be modified by ubiquitin. Using a novel peptide-based stable isotope labeling in cell culture (SILAC) approach, we show that specific lysine-less TCRα peptides become modified. In this study, we demonstrate that it is possible to detect both ester and thioester based ubiquitination events, although the exact linkage on lysine-less TCRα remains elusive. These findings demonstrate that SILAC can be used as a tool to identify modified peptides, even those with novel modifications that may not be detected using conventional proteomic work flows or informatics algorithms

The degradation of L-lysine in guinea pig liver homogenate: formation of alpha-aminoadipic acid

A summary of the little that is known of the metabolism of lysine in animals is as follows: it is indispensable in the diet, its α-amino group does not participate in reversible transamination reaction in vivo (2), neither the L nor D form is attacked by the appropriate amino acid oxidase, certain ε-nitrogen-substituted derivatives can replace lysine in the diet and their α-amino groups are oxidized by amino acid oxidases (3, 4), no α-nitrogen-substituted derivatives yet prepared can substitute for lysine in the diet (4-6)

Upregulation of Transglutaminase andε(γ-Glutamyl)-Lysine in the Fisher-Lewis Rat Model of Chronic Allograft Nephropathy

Background. Tissue transglutaminase (TG2), a cross-linking enzyme, modulates deposition of extracellular matrix protein in renal fibrosis. This study aimed to examine TG2 and its cross-link product ε(γ-glutamyl)-lysine in the Fisher-Lewis rat renal transplantation (RTx) model of chronic allograft nephropathy (CAN). Materials and Methods. Left renal grafts from male Fisher and Lewis were transplanted into Lewis rats, generating allografts and isografts, respectively. Blood pressure, renal function, and proteinuria were monitored for up to 52 weeks. At termination, CAN was assessed in the renal tissue by light and electron microscopy, TG2 and ε(γ-glutamyl)-lysine by immunofluorescence, and the urinary ε(γ-glutamyl)-lysine by high performance liquid chromatography. Results. Compared to the isograft, the allografts were hypertensive, proteinuric, and uraemic and developed CAN. Extracellular TG2 (glomerulus: 64.55 + 17.61 versus 2.11 + 0.17, P<0.001; interstitium: 13.72 + 1.62 versus 3.19 + 0.44, P<0.001), ε(γ-glutamyl)-lysine (glomerulus: 21.74 + 2.71 versus 1.98 + 0.37, P<0.01; interstitium: 37.96 + 17.06 versus 0.42 + 0.11, P<0.05), TG2 enzyme activity (1.09 + 0.13 versus 0.41 + 0.03 nmol/h/mg protein, P<0.05), TG2 mRNA (20-fold rise), and urinary ε(γ-glutamyl)-lysine (534.2 + 198.4 nmol/24 h versus 57.2 + 4.1 nmol/24 h,P<0.05) levels were significantly elevated in the allografts and showed a positive linear correlation with tubulointerstitial fibrosis. Conclusion. CAN was associated with upregulation of renal TG2 pathway, which has a potential for pharmacological intervention. The elevated urinary ε(γ-glutamyl)-lysine, measured for the first time in RTx, is a potential biomarker of CA

Alpha-aminoadipic acid: A product of lysine metabolism

As part of a study of protein and peptide metabolism lysine was synthesized with C14 in the ε position and resolved into the L and D isomers. 10 mg. of labeled lysine dihydrochloride (either L- or D-) and 0.66 gm. (wet weight) of guinea pig liver homogenate were added to a reaction mixture containing 1.3 per cent of an amino acid mixture corresponding to the composition of casein except for lysine and 0.01 M α-ketoglutarate, all in a final volume of 4 ml. of isotonic saline solution.(1) The reaction was carried out under oxygen for 6 hours at 38°

Treatment of Porphyromonas gulae infection and downstream pathology in the aged dog by lysine-gingipain inhibitor COR388.

COR388, a small-molecule lysine-gingipain inhibitor, is currently being investigated in a Phase 2/3 clinical trial for Alzheimer's disease (AD) with exploratory endpoints in periodontal disease. Gingipains are produced by two species of bacteria, Porphyromonas gingivalis and Porphyromonas gulae, typically associated with periodontal disease and systemic infections in humans and dogs, respectively. P. gulae infection in dogs is associated with periodontal disease, which provides a physiologically relevant model to investigate the pharmacology of COR388. In the current study, aged dogs with a natural oral infection of P. gulae and periodontal disease were treated with COR388 by oral administration for up to 90 days to assess lysine-gingipain target engagement and reduction of bacterial load and downstream pathology. In a 28-day dose-response study, COR388 inhibited the lysine-gingipain target and reduced P. gulae load in saliva, buccal cells, and gingival crevicular fluid. The lowest effective dose was continued for 90 days and was efficacious in continuous reduction of bacterial load and downstream periodontal disease pathology. In a separate histology study, dog brain tissue showed evidence of P. gulae DNA and neuronal lysine-gingipain, demonstrating that P. gulae infection is systemic and spreads beyond its oral reservoir, similar to recent observations of P. gingivalis in humans. Together, the pharmacokinetics and pharmacodynamics of COR388 lysine-gingipain inhibition, along with reduction of bacterial load and periodontal disease in naturally occurring P. gulae infection in the dog, support the use of COR388 in targeting lysine-gingipain and eliminating P. gingivalis infection in humans

Encapsulation of ascorbic acid promotes the reduction of Maillard reaction products in UHT milk

The presence of amino groups and carbonyls renders fortified milk with ascorbic acid particularly susceptible to the reduction of available lysine and to the formation of Maillard reaction products (MRPs), as Nε-(Carboxyethyl)-L-lysine (CEL), Nε-(Carboxymethyl)-L-lysine (CML), Amadori products (APs) and off-flavors. A novel approach was proposed to control the Maillard reaction (MR) in fortified milk: ascorbic acid was encapsulated in a lipid coating and the effects were tested after a lab scale UHT treatment. Encapsulation promoted a delayed release of ascorbic acid and a reduction in the formation of MRPs. Total lysine increased up to 45% in milk with encapsulated ascorbic acid, while reductions in CML, CEL and furosine ranged from 10% to 53% compared with control samples. The effects were also investigated towards the formation of amide-AGEs (advanced glycation end products) by high resolution mass spectrometry (HRMS) revealing that several mechanisms coincide with the MR in the presence of ascorbic acid (AA)

Single-phase feeding and compensatory growth in growing and finishing pigs (OK-Net Ecofeed Practice Abstract)

• Limit the supply of essential amino acids during early growth and utilise the pigs’ capacity to fully compensate for the restriction by increased protein retention and faster growth during later growth phases. • Crude protein and lysine contents can be substantially reduced, below common standards (i.e. crude protein to 16.5% and digestible lysine between 0.70-0.80 g standardised ileal digestible (SID) lysine/MJ NE), in well-balanced diets. • A reduction in crude protein content, from 15.5 to 14.5 g SID/g SID lysine can lower the nitrogen output by approximately 10%. • Formulate diets on a digestible amino acid basis rather than on a total amino acid or crude protein basis. • High-quality protein feed ingredients such as faba beans, peas, oil seed-, dairy- and cereal-based by-products, aquatic resources, etc., or a combination of them, can be used. • At the pig level, this practice can reduce soya bean cake utilisation (14%) and increase pea utilisation (22%). • Careful follow-up of the pigs' feed consumption, growth and health status is recommended

Incorporation in vitro of labeled amino acids into bone marrow cell proteins

Nearly all experiments on the incorporation of labeled amino acids into tissue proteins in vitro have been done on tissues whose cell structure has been partially or completely disintegrated, e.g. tissue slices, segments, or homogenates. Since cell destruction reduces or abolishes the uptake of labeled amino acids (1), it seemed worth while to carry out studies on intact cells in vitro. Bone marrow cells were found to be suitable for this purpose. The labeled amino acids used were glycine-1-C14, L-leucine-1-C14, L-lysine-1-C14, and L-lysine-6-C14

Effect of bet missense mutations on bromodomain function, inhibitor binding and stability

Lysine acetylation is an important epigenetic mark regulating gene transcription and chromatin structure. Acetylated lysine residues are specifically recognized by bromodomains, small protein interaction modules that read these modification in a sequence and acetylation dependent way regulating the recruitment of transcriptional regulators and chromatin remodelling enzymes to acetylated sites in chromatin. Recent studies revealed that bromodomains are highly druggable protein interaction domains resulting in the development of a large number of bromodomain inhibitors. BET bromodomain inhibitors received a lot of attention in the oncology field resulting in the rapid translation of early BET bromodomain inhibitors into clinical studies. Here we investigated the effects of mutations present as polymorphism or found in cancer on BET bromodomain function and stability and the influence of these mutants on inhibitor binding. We found that most BET missense mutations localize to peripheral residues in the two terminal helices. Crystal structures showed that the three dimensional structure is not compromised by these mutations but mutations located in close proximity to the acetyl-lysine binding site modulate acetyl-lysine and inhibitor binding. Most mutations affect significantly protein stability and tertiary structure in solution, suggesting new interactions and an alternative network of protein-protein interconnection as a consequence of single amino acid substitution. To our knowledge this is the first report studying the effect of mutations on bromodomain function and inhibitor binding